##fileformat=VCFv4.1
##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="RMS Mapping Quality">
##FORMAT=<ID=VF,Number=1,Type=Float,Description="Variant Frequency, the ratio of the sum of the called variant depth to the total depth">
##INFO=<ID=TI,Number=.,Type=String,Description="Transcript ID">
##INFO=<ID=GI,Number=.,Type=String,Description="Gene ID">
##INFO=<ID=EXON,Number=0,Type=Flag,Description="Exon Region">
##INFO=<ID=FC,Number=.,Type=String,Description="Functional Consequence">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record">
##INFO=<ID=BLOCKAVG_min30p3a,Number=0,Type=Flag,Description="Non-variant site block. All sites in a block are constrained to be non-variant, have the same filter value, and have all sample values in range [x,y] , y <= max(x+3,(x*(1+0.3))). All printed site block sample values are the minimum observed in the region spanned by the block">
##FILTER=<ID=LowGQX,Description="Locus GQX is less than 10.0000 or not present">
##FILTER=<ID=LowVariantFreq,Description="Low variant frequency < 0.20">
##FILTER=<ID=LowGQ,Description="GQ below < 30.00">
##FILTER=<ID=R8,Description="IndelRepeatLength is greater than 8">
##FILTER=<ID=SB,Description="Strand bias (SB) is greater than than -10">
##FILTER=<ID=LowDP,Description="Depth (DP) is less than 20">
##FILTER=<ID=IndelConflict,Description="Locus is in region with conflicting indel calls.">
##FILTER=<ID=SiteConflict,Description="Site genotype conflicts with proximal indel call. This is typically a heterozygous SNV call made inside of a heterozygous deletion.">
##FILTER=<ID=LowMQ,Description="Site MQ is less than 0.0000">
##FILTER=<ID=LowQD,Description="Locus QD is less than 0.0000">
##annotator=MARS
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[D:\Illumina\MiSeqAnalysis\200417_M04358_0133_000000000-CV8CW\Data\Intensities\BaseCalls\Alignment\20165-01-01_S19.bam] read_buffer_size=null phone_home=NO_ET gatk_key=null read_filter=[] intervals=[D:\Illumina\MiSeqAnalysis\200417_M04358_0133_000000000-CV8CW\Data\Intensities\BaseCalls\Alignment\Segment_intervals_M2.0.picard] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=C:\Illumina\MiSeq Reporter\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA\genome.fa nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=5000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=-1 defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=OFF log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=1.0 standard_min_confidence_threshold_for_emitting=30.0 noSLOD=false annotateNDA=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 max_alternate_alleles=3 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 noBandedIndel=false indelDebug=false ignoreSNPAlleles=false includeGVCFData=true dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr10,length=135534747>
##contig=<ID=chr11,length=135006516>
##contig=<ID=chr12,length=133851895>
##contig=<ID=chr13,length=115169878>
##contig=<ID=chr14,length=107349540>
##contig=<ID=chr15,length=102531392>
##contig=<ID=chr16,length=90354753>
##contig=<ID=chr17,length=81195210>
##contig=<ID=chr18,length=78077248>
##contig=<ID=chr19,length=59128983>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr20,length=63025520>
##contig=<ID=chr21,length=48129895>
##contig=<ID=chr22,length=51304566>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4,length=191154276>
##contig=<ID=chr5,length=180915260>
##contig=<ID=chr6,length=171115067>
##contig=<ID=chr7,length=159138663>
##contig=<ID=chr8,length=146364022>
##contig=<ID=chr9,length=141213431>
##contig=<ID=chrM,length=16571>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
##reference=file://C:\Illumina\MiSeq Reporter\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA\genome.fa
##gvcftools_version="0.12.1"
##gvcftools_cmdline="C:\Illumina\MiSeq Reporter\Workflows\EnrichmentWorker\gatk_to_gvcf.exe --no-default-filters --min-qd 0.0000 --min-gqx 10.0000 --min-mq 0.0000"
##source=GATK 1.6
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	20165-01-01
chr1	1853615	.	T	TCTGA	43048.90	PASS	DP=655;FS=0.000;HRun=0;HaplotypeScore=378.4853;MQ=60;MQ0=0;QD=65.72;SB=-21472.25	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:31,604:655:99:43049,1881,0:60:99:0.951
chr1	1854109	rs2803348	A	G	6367.78	PASS	BaseQRankSum=4.683;DP=578;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=13.7144;MQ=60;MQ0=0;MQRankSum=0.499;QD=11.02;ReadPosRankSum=1.014;SB=-4308.25	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:308,269:578:99:6368,0,7679:60:99:0.466
chr1	1861582	rs2803295	C	T	11449.97	PASS	BaseQRankSum=4.963;DP=923;Dels=0.00;FS=9.590;HRun=0;HaplotypeScore=43.4575;MQ=60;MQ0=0;MQRankSum=1.107;QD=12.41;ReadPosRankSum=1.317;SB=-7457.88	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:447,475:923:99:11450,0,10796:60:99:0.515
chr1	1873453	rs2748981	G	A	3777.41	PASS	BaseQRankSum=2.837;DP=348;Dels=0.00;FS=1.831;HRun=0;HaplotypeScore=8.4407;MQ=60;MQ0=0;MQRankSum=0.196;QD=10.85;ReadPosRankSum=0.572;SB=-1832.91	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:195,153:348:99:3777,0,4672:60:99:0.440
chr1	1873514	rs2803326	A	G	6065.38	PASS	BaseQRankSum=3.459;DP=564;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=27.3531;MQ=60;MQ0=0;MQRankSum=-1.282;QD=10.75;ReadPosRankSum=-0.270;SB=-4264.38	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:304,260:564:99:6065,0,7288:60:99:0.461
chr1	1873525	rs2803327	T	C	5943.92	PASS	BaseQRankSum=2.660;DP=571;Dels=0.00;FS=1.334;HRun=0;HaplotypeScore=34.4799;MQ=60;MQ0=0;MQRankSum=0.851;QD=10.41;ReadPosRankSum=0.869;SB=-4218.39	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:311,260:571:99:5944,0,7445:60:99:0.455
chr1	1875858	rs2803336	C	G	4565.49	PASS	BaseQRankSum=1.668;DP=555;Dels=0.00;FS=8.033;HRun=0;HaplotypeScore=17.9529;MQ=60;MQ0=0;MQRankSum=2.889;QD=8.23;ReadPosRankSum=1.706;SB=-2690.89	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:349,204:554:99:4565,0,8408:60:99:0.369
chr1	1875859	rs2803337	A	G	4385.89	PASS	BaseQRankSum=2.936;DP=550;Dels=0.00;FS=6.058;HRun=0;HaplotypeScore=17.9529;MQ=60;MQ0=0;MQRankSum=2.017;QD=7.97;ReadPosRankSum=1.764;SB=-2717.41	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:348,202:550:99:4386,0,8350:60:99:0.367
chr1	1884735	.	CT	C	378.71	R8	BaseQRankSum=-0.048;DP=182;FS=2.869;HRun=16;HaplotypeScore=720.0460;MQ=60;MQ0=0;MQRankSum=1.463;QD=2.08;ReadPosRankSum=1.005;SB=-181.26	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:125,32:182:99:418,0,1825:60:99:0.204
chr1	1885055	rs2474455	C	T	3844.75	PASS	BaseQRankSum=0.938;DP=411;Dels=0.00;FS=0.757;HRun=0;HaplotypeScore=8.8860;MQ=60;MQ0=0;MQRankSum=0.401;QD=9.35;ReadPosRankSum=0.144;SB=-2527.17;TI=NM_001080484;GI=KIAA1751;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:246,165:411:99:3845,0,5626:60:99:0.401
chr1	1886222	rs2803287	T	G	6798.68	PASS	BaseQRankSum=5.790;DP=612;Dels=0.00;FS=0.293;HRun=0;HaplotypeScore=27.5713;MQ=60;MQ0=0;MQRankSum=0.661;QD=11.11;ReadPosRankSum=0.427;SB=-4394.96;TI=NM_001080484;GI=KIAA1751;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:318,293:612:99:6799,0,7258:60:99:0.480
chr1	1886385	rs2803286	T	C	8760.13	PASS	BaseQRankSum=4.693;DP=779;Dels=0.00;FS=3.711;HRun=0;HaplotypeScore=22.2803;MQ=60;MQ0=0;MQRankSum=0.821;QD=11.25;ReadPosRankSum=-0.809;SB=-6171.89;TI=NM_001080484;GI=KIAA1751;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:400,378:779:99:8760,0,9608:60:99:0.486
chr1	1886501	rs2748976	C	A	1686.78	PASS	BaseQRankSum=1.807;DP=673;Dels=0.00;FS=28.233;HRun=0;HaplotypeScore=34.0081;MQ=59;MQ0=5;MQRankSum=-0.322;QD=2.51;ReadPosRankSum=3.747;SB=-996.35;TI=NM_001080484;GI=KIAA1751;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:529,144:673:99:1717,0,12130:59:99:0.214
chr1	1886519	rs2748975	C	A	2922.07	PASS	BaseQRankSum=1.028;DP=641;Dels=0.00;FS=17.757;HRun=0;HaplotypeScore=46.7892;MQ=59;MQ0=5;MQRankSum=1.282;QD=4.56;ReadPosRankSum=7.023;SB=-2031.03;TI=NM_001080484;GI=KIAA1751;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:453,188:641:99:2952,0,10677:59:99:0.293
chr1	1887019	rs28548017	A	G	5512.11	PASS	BaseQRankSum=0.823;DP=575;Dels=0.00;FS=0.637;HRun=2;HaplotypeScore=39.8142;MQ=60;MQ0=0;MQRankSum=3.407;QD=9.59;ReadPosRankSum=0.861;SB=-3344.84;TI=NM_001080484;GI=KIAA1751;FC=Missense_X763Q;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:349,225:575:99:5512,0,8531:60:99:0.392
chr1	1900186	rs35269416	T	C	2922.07	PASS	BaseQRankSum=2.938;DP=332;Dels=0.00;FS=10.617;HRun=0;HaplotypeScore=18.9636;MQ=60;MQ0=0;MQRankSum=0.661;QD=8.80;ReadPosRankSum=0.340;SB=-1607.75;TI=NM_001080484;GI=KIAA1751;FC=Missense_K378R;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:205,127:332:99:2952,0,4784:60:99:0.383
chr1	1900232	rs16824588	T	C	2089.97	PASS	BaseQRankSum=2.815;DP=262;Dels=0.00;FS=5.693;HRun=0;HaplotypeScore=11.2065;MQ=60;MQ0=0;MQRankSum=-0.221;QD=7.98;ReadPosRankSum=-1.594;SB=-787.01;TI=NM_001080484;GI=KIAA1751;FC=Missense_I363V;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:172,90:262:99:2120,0,4523:60:99:0.344
chr1	1918488	rs4350140	A	G	5399.44	PASS	BaseQRankSum=0.071;DP=449;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=17.3091;MQ=60;MQ0=0;MQRankSum=0.363;QD=12.03;ReadPosRankSum=1.285;SB=-3335.25;TI=NM_001080484;GI=KIAA1751;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:216,232:449:99:5399,0,5210:60:99:0.518
chr1	38030696	rs6619	T	C	5293.70	PASS	BaseQRankSum=3.368;DP=446;Dels=0.00;FS=0.342;HRun=1;HaplotypeScore=11.2012;MQ=60;MQ0=0;MQRankSum=0.588;QD=11.87;ReadPosRankSum=-1.018;SB=-3632.10;TI=NM_003462;GI=DNALI1;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:224,222:446:99:5294,0,5028:60:99:0.498
chr1	78578177	rs6666954	T	C	2961.87	PASS	BaseQRankSum=-1.050;DP=397;Dels=0.00;FS=4.007;HRun=0;HaplotypeScore=13.5768;MQ=60;MQ0=0;MQRankSum=0.393;QD=7.46;ReadPosRankSum=1.113;SB=-2017.22;TI=NM_017655;GI=GIPC2;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:257,138:397:99:2992,0,6301:60:99:0.349
chr1	118644430	rs10754367	A	G	10939.35	PASS	DP=398;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=10.0839;MQ=60;MQ0=0;QD=27.49;SB=-7705.07;TI=NM_206996;GI=SPAG17;FC=Synonymous_N189N;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,398:398:99:10939,777,0:60:99:1.000
chr1	156495177	rs41267369	A	G	3926.66	PASS	BaseQRankSum=-0.657;DP=324;Dels=0.00;FS=0.419;HRun=0;HaplotypeScore=27.8479;MQ=60;MQ0=0;MQRankSum=-0.380;QD=12.12;ReadPosRankSum=0.620;SB=-2176.36	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:157,164:324:99:3927,0,3702:60:99:0.511
chr1	156495639	rs77821780	C	T	3120.09	PASS	BaseQRankSum=0.096;DP=309;Dels=0.00;FS=0.431;HRun=0;HaplotypeScore=17.5032;MQ=59;MQ0=0;MQRankSum=-0.370;QD=10.10;ReadPosRankSum=-1.189;SB=-1665.37;TI=NM_178229;GI=IQGAP3;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:182,125:309:99:3150,0,4447:59:99:0.407
chr1	156496188	rs6427315	A	G	15204.81	PASS	BaseQRankSum=1.685;DP=521;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=32.3333;MQ=60;MQ0=0;MQRankSum=1.093;QD=29.18;ReadPosRankSum=-0.779;SB=-9567.96;TI=NM_178229;GI=IQGAP3;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:1,519:521:99:15205,1099,0:60:99:0.998
chr1	156499969	rs1171566	T	C	8170.23	PASS	BaseQRankSum=5.355;DP=735;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=36.8885;MQ=60;MQ0=0;MQRankSum=0.308;QD=11.12;ReadPosRankSum=-0.979;SB=-5963.49;TI=NM_178229;GI=IQGAP3;FC=Synonymous_L1444L;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:368,366:735:99:8170,0,8591:60:99:0.499
chr1	156500096	.	T	C	3368.15	PASS	BaseQRankSum=2.126;DP=283;Dels=0.00;FS=0.468;HRun=1;HaplotypeScore=15.6936;MQ=60;MQ0=0;MQRankSum=1.550;QD=11.90;ReadPosRankSum=0.949;SB=-1464.55;TI=NM_178229;GI=IQGAP3;FC=Missense_K1402R;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:146,136:283:99:3368,0,3890:60:99:0.482
chr1	156502870	rs4661044	C	T	7588.75	PASS	BaseQRankSum=5.859;DP=731;Dels=0.00;FS=1.165;HRun=0;HaplotypeScore=35.5633;MQ=60;MQ0=0;MQRankSum=-0.648;QD=10.38;ReadPosRankSum=-1.775;SB=-5393.33;TI=NM_178229;GI=IQGAP3;FC=Synonymous_T1335T;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:398,332:731:99:7589,0,9295:60:99:0.455
chr1	156526387	rs11264498	C	G	8701.86	PASS	BaseQRankSum=1.165;DP=688;Dels=0.00;FS=1.909;HRun=0;HaplotypeScore=30.2815;MQ=60;MQ0=0;MQRankSum=1.314;QD=12.65;ReadPosRankSum=0.894;SB=-5811.34;TI=NM_178229;GI=IQGAP3;FC=Missense_V410L;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:321,367:688:99:8702,0,7522:60:99:0.533
chr1	156526444	rs2488269	T	C	16134.25	PASS	DP=577;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=31.5153;MQ=60;MQ0=0;QD=27.96;SB=-9498.29;TI=NM_178229;GI=IQGAP3;FC=Missense_R391G;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,574:577:99:16134,1153,0:60:99:1.000
chr1	156532908	rs16837492	C	A	9064.06	PASS	BaseQRankSum=2.417;DP=306;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=5.4599;MQ=60;MQ0=0;MQRankSum=-1.319;QD=29.62;ReadPosRankSum=1.423;SB=-3654.03;TI=NM_178229;GI=IQGAP3;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:2,304:306:99:9064,653,0:60:99:0.993
chr1	156532977	rs1171547	T	C	17009.32	PASS	BaseQRankSum=2.403;DP=638;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=18.3416;MQ=60;MQ0=0;MQRankSum=-0.152;QD=26.66;ReadPosRankSum=-1.070;SB=-10998.24;TI=NM_178229;GI=IQGAP3;FC=Synonymous_Q249Q;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:2,636:638:99:17009,1198,0:60:99:0.997
chr1	156536221	rs2066377	G	C	10740.85	PASS	DP=388;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=9.9097;MQ=60;MQ0=0;QD=27.68;SB=-6439.01;TI=NM_178229;GI=IQGAP3;FC=Synonymous_P81P;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,388:388:99:10741,762,0:60:99:1.000
chr1	156536251	rs947662	T	C	13155.91	PASS	DP=491;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=10.2122;MQ=60;MQ0=0;QD=26.79;SB=-9171.53;TI=NM_178229;GI=IQGAP3;FC=Synonymous_L71L;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,491:491:99:13156,927,0:60:99:1.000
chr1	156536353	rs947663	A	G	9032.24	PASS	DP=310;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=5.5353;MQ=60;MQ0=0;QD=29.14;SB=-4449.40;TI=NM_178229;GI=IQGAP3;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,310:310:99:9032,650,0:60:99:1.000
chr1	156539154	rs6427319	T	C	12674.56	PASS	DP=491;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=22.7069;MQ=60;MQ0=0;QD=25.81;SB=-9403.04;TI=NM_178229;GI=IQGAP3;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,489:491:99:12675,888,0:60:99:1.000
chr1	159860259	rs2501320	G	A	4795.08	PASS	BaseQRankSum=2.582;DP=427;Dels=0.00;FS=6.449;HRun=0;HaplotypeScore=18.0588;MQ=60;MQ0=0;MQRankSum=0.524;QD=11.23;ReadPosRankSum=1.114;SB=-2158.63;TI=NM_012337;GI=CCDC19;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:237,190:427:99:4795,0,5746:60:99:0.445
chr1	245133539	rs7542813	A	G	5792.11	PASS	DP=216;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=16.8466;MQ=60;MQ0=0;QD=26.82;SB=-3465.64;TI=NM_032328,NR_026586;GI=EFCAB2,EFCAB2;FC=Silent,Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,216:216:99:5792,412,0:60:99:1.000
chr1	245245378	rs10927386	T	C	3550.46	PASS	DP=121;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=3.5489;MQ=60;MQ0=0;QD=29.34;SB=-1506.37;TI=NM_032328,NR_026586,NR_026588,NM_001143943,NR_026587;GI=EFCAB2,EFCAB2,EFCAB2,EFCAB2,EFCAB2;FC=Silent,Silent,Silent,Silent,Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,121:121:99:3550,256,0:60:99:1.000
chr1	245245402	rs10927387	C	T	4665.50	PASS	DP=155;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.6823;MQ=60;MQ0=0;QD=30.10;SB=-2152.02;TI=NM_032328,NR_026586,NR_026588,NM_001143943,NR_026587;GI=EFCAB2,EFCAB2,EFCAB2,EFCAB2,EFCAB2;FC=Synonymous_P67P,Silent,Silent,Synonymous_P67P,Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,155:155:99:4665,337,0:60:99:1.000
chr1	245251020	rs1047707	G	T	8418.80	PASS	DP=289;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=7.4582;MQ=60;MQ0=0;QD=29.13;SB=-5454.45;TI=NM_032328,NR_026586,NR_026588,NM_001143943,NR_026587;GI=EFCAB2,EFCAB2,EFCAB2,EFCAB2,EFCAB2;FC=Silent,Silent,Silent,Silent,Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,288:289:99:8419,605,0:60:99:1.000
chr1	245251140	rs4658695	T	G	4663.49	PASS	DP=172;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=6.3643;MQ=60;MQ0=0;QD=27.11;SB=-3006.61;TI=NM_032328,NR_026586,NR_026588,NM_001143943,NR_026587;GI=EFCAB2,EFCAB2,EFCAB2,EFCAB2,EFCAB2;FC=Silent,Silent,Silent,Silent,Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,172:172:99:4663,328,0:60:99:1.000
chr1	245286313	rs4658701	G	A	10438.17	PASS	DP=342;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=10.8897;MQ=60;MQ0=0;QD=30.52;SB=-6043.68;TI=NR_026586,NM_001143943,NR_026587;GI=EFCAB2,EFCAB2,EFCAB2;FC=Silent,Silent,Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,340:342:99:10438,764,0:60:99:1.000
chr2	26647277	rs7423300	T	G	12187.01	PASS	BaseQRankSum=1.660;DP=436;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=21.1856;MQ=60;MQ0=0;MQRankSum=0.418;QD=27.95;ReadPosRankSum=0.299;SB=-6536.67;TI=NM_145038;GI=C2orf39;FC=Synonymous_A165A;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:1,434:436:99:12187,862,0:60:99:0.998
chr2	26667130	rs3795958	A	G	10190.28	PASS	DP=384;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=13.4491;MQ=60;MQ0=0;QD=26.54;SB=-6145.00;TI=NM_145038;GI=C2orf39;FC=Missense_K357E;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,384:384:99:10190,719,0:60:99:1.000
chr2	26667615	rs61509377	T	C	12862.19	PASS	DP=470;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=31.4028;MQ=60;MQ0=0;QD=27.37;SB=-8710.54;TI=NM_145038;GI=C2orf39;FC=Missense_W399R;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,469:470:99:12862,909,0:60:99:1.000
chr2	26671544	rs4072407	A	G	12796.15	PASS	DP=447;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=16.2383;MQ=60;MQ0=0;QD=28.63;SB=-6644.57;TI=NM_145038;GI=C2orf39;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,446:447:99:12796,915,0:60:99:1.000
chr2	26676322	rs1402962	A	G	17536.98	PASS	BaseQRankSum=1.709;DP=616;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=54.5635;MQ=60;MQ0=0;MQRankSum=-1.275;QD=28.47;ReadPosRankSum=1.709;SB=-10909.72;TI=NM_145038;GI=C2orf39;FC=Synonymous_E608E;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:1,613:616:99:17537,1264,0:60:99:0.998
chr2	68357264	.	T	A	13.64	LowVariantFreq;SB;LowDP	BaseQRankSum=-0.948;DP=18;Dels=0.00;FS=5.653;HRun=0;HaplotypeScore=8.7531;MQ=59;MQ0=0;MQRankSum=0.000;QD=0.76;ReadPosRankSum=-2.725;SB=-7.54	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:15,3:18:43.44:43,0,419:59:14:0.167
chr2	68357266	.	G	GT	69.67	R8;LowDP	BaseQRankSum=-1.200;DP=15;FS=0.000;HRun=14;HaplotypeScore=118.0634;MQ=58;MQ0=0;MQRankSum=-0.555;QD=4.64;ReadPosRankSum=0.660;SB=-33.43	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:7,6:15:77.43:109,0,77:58:70:0.462
chr2	68358046	.	CT	C	563.10	R8	BaseQRankSum=-1.616;DP=217;FS=0.000;HRun=21;HaplotypeScore=892.8789;MQ=60;MQ0=0;MQRankSum=-0.461;QD=2.59;ReadPosRankSum=-1.202;SB=-207.74;TI=NM_138458;GI=WDR92;FC=Noncoding;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:120,34:217:99:602,0,929:60:99:0.221
chr2	68358341	rs62145930	T	C	5054.70	PASS	BaseQRankSum=2.951;DP=480;Dels=0.00;FS=7.130;HRun=0;HaplotypeScore=9.1812;MQ=60;MQ0=0;MQRankSum=0.340;QD=10.53;ReadPosRankSum=-0.753;SB=-3350.63;TI=NM_138458;GI=WDR92;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:266,213:479:99:5055,0,7001:60:99:0.445
chr2	68364478	rs13009282	T	C	402.13	PASS	BaseQRankSum=0.163;DP=69;Dels=0.00;FS=2.219;HRun=0;HaplotypeScore=0.9159;MQ=60;MQ0=0;MQRankSum=2.550;QD=5.83;ReadPosRankSum=-2.276;SB=-229.02;TI=NM_138458;GI=WDR92;FC=Missense_M241V;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:48,21:69:99:432,0,1128:60:99:0.304
chr2	120303820	rs2579624	A	T	3132.77	PASS	BaseQRankSum=-0.467;DP=364;Dels=0.00;FS=2.941;HRun=0;HaplotypeScore=20.3422;MQ=60;MQ0=0;MQRankSum=0.104;QD=8.61;ReadPosRankSum=0.624;SB=-1662.12;TI=NM_001029996;GI=PCDP1;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:225,139:364:99:3163,0,5252:60:99:0.382
chr2	120317621	.	CTT	C	518.95	LowVariantFreq;R8	BaseQRankSum=1.667;DP=142;FS=2.610;HRun=20;HaplotypeScore=466.8791;MQ=60;MQ0=0;MQRankSum=-0.206;QD=3.65;ReadPosRankSum=-0.206;SB=-146.99;TI=NM_001029996;GI=PCDP1;FC=Noncoding	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:75,18:142:99:558,0,1374:60:99:0.194
chr2	120366057	rs11398750	G	GT	1774.72	R8	BaseQRankSum=-1.424;DP=124;FS=0.000;HRun=12;HaplotypeScore=265.2529;MQ=60;MQ0=0;MQRankSum=-1.239;QD=14.31;ReadPosRankSum=1.693;SB=-701.73;TI=NM_001029996;GI=PCDP1;FC=Noncoding	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:23,79:124:99:1814,0,229:60:99:0.775
chr2	120369300	rs10864986	T	C	6852.79	PASS	DP=243;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=8.0324;MQ=60;MQ0=0;QD=28.20;SB=-4112.34;TI=NM_001029996;GI=PCDP1;FC=Synonymous_V145V;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,243:243:99:6853,488,0:60:99:1.000
chr2	120383138	rs77292092	CATT	C	7922.76	PASS	BaseQRankSum=0.330;DP=280;FS=2.630;HRun=0;HaplotypeScore=163.4233;MQ=61;MQ0=0;MQRankSum=2.160;QD=28.30;ReadPosRankSum=0.340;SB=-3441.74;TI=NM_001029996;GI=PCDP1;FC=Noncoding	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:129,151:280:99:7923,0,6899:61:99:0.539
chr2	120388412	rs2272058	G	A	13884.64	PASS	DP=509;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=19.4635;MQ=60;MQ0=0;QD=27.28;SB=-8301.81;TI=NM_001029996;GI=PCDP1;FC=Missense_V351I;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,509:509:99:13885,984,0:60:99:1.000
chr2	120404629	.	ATT	A,AT	4833.54	R8	BaseQRankSum=-1.759;DP=259;FS=1.126;HaplotypeScore=313.3865;MQ=60;MQ0=0;MQRankSum=0.141;QD=18.66;ReadPosRankSum=-0.244;SB=-1840.99;TI=NM_001029996;GI=PCDP1;FC=Noncoding	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/2:43,53,0:259:99:4834,2987,3264,1146,0,819:60:99:0.552
chr2	120414083	rs6761357	C	T	13462.75	PASS	DP=465;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=15.2808;MQ=60;MQ0=0;QD=28.95;SB=-9141.23;TI=NM_001029996;GI=PCDP1;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,465:465:99:13463,963,0:60:99:1.000
chr2	147596973	rs4411641	A	G	528.37	PASS	DP=21;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=60;MQ0=0;QD=25.16;SB=-356.30	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,21:21:39.13:561,39,0:60:39:1.000
chr2	219545309	rs2303565	T	C	6088.20	PASS	BaseQRankSum=4.484;DP=539;Dels=0.00;FS=2.229;HRun=4;HaplotypeScore=17.3004;MQ=60;MQ0=0;MQRankSum=-1.227;QD=11.30;ReadPosRankSum=-0.461;SB=-3874.47;TI=NM_015690;GI=STK36;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:266,271:539:99:6088,0,6147:60:99:0.505
chr2	219553503	rs73079060	T	C	7541.43	PASS	BaseQRankSum=0.063;DP=715;Dels=0.00;FS=0.554;HRun=0;HaplotypeScore=22.1335;MQ=60;MQ0=0;MQRankSum=-0.870;QD=10.55;ReadPosRankSum=-0.230;SB=-5252.48;TI=NM_015690;GI=STK36;FC=Synonymous_D488D;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:377,338:715:99:7541,0,8842:60:99:0.473
chr2	219555292	rs1427444	A	G	3562.00	PASS	BaseQRankSum=-0.570;DP=329;Dels=0.00;FS=2.432;HRun=0;HaplotypeScore=14.6277;MQ=60;MQ0=0;MQRankSum=0.801;QD=10.83;ReadPosRankSum=1.128;SB=-1843.89;TI=NM_015690;GI=STK36;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:178,150:329:99:3562,0,4278:60:99:0.457
chr2	219557014	rs6709303	A	C	2553.22	PASS	BaseQRankSum=0.836;DP=214;Dels=0.00;FS=1.082;HRun=4;HaplotypeScore=6.3944;MQ=60;MQ0=0;MQRankSum=0.498;QD=11.93;ReadPosRankSum=-0.889;SB=-1397.56;TI=NM_015690;GI=STK36;FC=Missense_Q638P;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:110,104:214:99:2583,0,2598:60:99:0.486
chr2	219562677	rs55633575	G	A	3888.10	PASS	BaseQRankSum=0.394;DP=411;Dels=0.00;FS=5.721;HRun=0;HaplotypeScore=10.7913;MQ=60;MQ0=0;MQRankSum=2.070;QD=9.46;ReadPosRankSum=2.272;SB=-2409.16;TI=NM_015690;GI=STK36;FC=Missense_V1004I;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:243,167:411:99:3888,0,5989:60:99:0.407
chr2	219563496	rs58753698	T	C	6604.09	PASS	BaseQRankSum=3.287;DP=526;Dels=0.00;FS=1.009;HRun=0;HaplotypeScore=27.0981;MQ=60;MQ0=0;MQRankSum=0.011;QD=12.56;ReadPosRankSum=-0.184;SB=-3807.96;TI=NM_015690;GI=STK36;FC=Synonymous_L1077L;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:278,248:526:99:6604,0,7017:60:99:0.471
chr2	219563958	rs73079079	T	G	5706.48	PASS	BaseQRankSum=1.762;DP=656;Dels=0.00;FS=1.259;HRun=1;HaplotypeScore=18.9988;MQ=60;MQ0=0;MQRankSum=0.993;QD=8.70;ReadPosRankSum=2.210;SB=-4010.96;TI=NM_015690;GI=STK36;FC=Missense_C1231G;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:394,261:656:99:5706,0,9536:60:99:0.398
chr2	219567043	rs80263269	A	G	5224.96	PASS	BaseQRankSum=3.231;DP=553;Dels=0.00;FS=1.006;HRun=0;HaplotypeScore=21.8878;MQ=60;MQ0=0;MQRankSum=0.574;QD=9.45;ReadPosRankSum=-1.172;SB=-3168.69;TI=NM_015690;GI=STK36;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:327,226:553:99:5225,0,7807:60:99:0.409
chr3	60898434	rs11130795	T	C	492.86	LowVariantFreq	BaseQRankSum=1.049;DP=227;Dels=0.00;FS=0.675;HRun=0;HaplotypeScore=3.5764;MQ=60;MQ0=0;MQRankSum=-0.938;QD=2.17;ReadPosRankSum=-1.177;SB=-353.31;TI=NM_002012,NM_001166243;GI=FHIT,FHIT;FC=Silent,Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:190,36:227:99:523,0,4322:60:99:0.159
chr3	126142496	rs13064828	T	C	12824.49	PASS	DP=453;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=25.5656;MQ=60;MQ0=0;QD=28.31;SB=-6298.90;TI=NM_182628;GI=CCDC37;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,450:453:99:12824,921,0:60:99:1.000
chr3	127783698	rs1044843	A	T	2259.21	PASS	BaseQRankSum=3.658;DP=221;Dels=0.00;FS=5.755;HRun=1;HaplotypeScore=22.8213;MQ=60;MQ0=0;MQRankSum=-1.329;QD=10.22;ReadPosRankSum=2.096;SB=-1039.45;TI=NM_013336;GI=SEC61A1;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:128,93:221:99:2289,0,2981:60:99:0.421
chr3	127799835	rs68118584	TAGAG	T	6835.10	R8	BaseQRankSum=-0.545;DP=297;FS=0.432;HRun=0;HaplotypeScore=176.4017;MQ=60;MQ0=0;MQRankSum=0.040;QD=23.01;ReadPosRankSum=1.763;SB=-2966.39;TI=NM_003707;GI=RUVBL1;FC=Noncoding;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:168,120:297:99:6835,0,9260:60:99:0.417
chr3	127799983	rs1057220	A	C	7123.61	PASS	BaseQRankSum=6.587;DP=630;Dels=0.00;FS=1.263;HRun=2;HaplotypeScore=16.1845;MQ=60;MQ0=0;MQRankSum=0.267;QD=11.31;ReadPosRankSum=1.699;SB=-4770.80;TI=NM_003707;GI=RUVBL1;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:326,303:629:99:7124,0,7851:60:99:0.482
chr3	127800071	rs1057156	A	G	7834.73	PASS	BaseQRankSum=5.743;DP=722;Dels=0.00;FS=4.877;HRun=0;HaplotypeScore=25.9591;MQ=60;MQ0=0;MQRankSum=-1.616;QD=10.85;ReadPosRankSum=0.533;SB=-4980.98;TI=NM_003707;GI=RUVBL1;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:393,328:722:99:7835,0,9742:60:99:0.455
chr3	127872506	rs11711710	C	T	3006.09	PASS	BaseQRankSum=2.574;DP=324;Dels=0.00;FS=1.848;HRun=2;HaplotypeScore=13.1995;MQ=60;MQ0=0;MQRankSum=-0.251;QD=9.28;ReadPosRankSum=2.275;SB=-2408.31;TI=NM_021937;GI=EEFSEC;FC=Synonymous_G52G;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:171,153:324:99:3036,0,3412:60:99:0.472
chr3	127872602	rs11719546	A	G	1053.87	PASS	BaseQRankSum=0.202;DP=182;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=18.0578;MQ=60;MQ0=0;MQRankSum=1.774;QD=5.79;ReadPosRankSum=-2.236;SB=-759.68;TI=NM_021937;GI=EEFSEC;FC=Synonymous_P84P;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:123,58:182:99:1084,0,2739:60:99:0.320
chr3	166960278	rs11923256	G	T	7290.92	PASS	DP=273;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=6.2804;MQ=60;MQ0=0;QD=26.71;SB=-4246.65;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Silent,Silent,Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,273:273:99:7291,515,0:60:99:1.000
chr3	167023738	rs13096767	G	C	6033.21	PASS	DP=212;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=3.5764;MQ=60;MQ0=0;QD=28.46;SB=-3009.00;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Unknown_444,Unknown_473,Unknown_473;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,212:212:99:6033,430,0:60:99:1.000
chr3	167034814	rs13068132	T	C	1633.38	PASS	DP=60;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=60;MQ0=0;QD=27.22;SB=-1005.78;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Synonymous_L362L,Synonymous_L391L,Synonymous_L391L;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,60:60:99:1666,117,0:60:99:1.000
chr3	167051769	rs11923054	T	C	4146.54	PASS	DP=130;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8941;MQ=60;MQ0=0;QD=31.90;SB=-1294.58;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Missense_K149R,Missense_K178R,Missense_K178R;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,130:130:99:4147,304,0:60:99:1.000
chr3	167068256	rs4619784	T	A	10674.69	PASS	DP=389;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=8.0468;MQ=60;MQ0=0;QD=27.44;SB=-7265.18;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Missense_K131N,Missense_K160N,Missense_K160N;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,389:389:99:10675,756,0:60:99:1.000
chr3	167077691	rs4257551	T	A	7584.01	PASS	DP=252;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=4.5758;MQ=60;MQ0=0;QD=30.10;SB=-3237.09;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Synonymous_V104V,Synonymous_V133V,Synonymous_V133V;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,252:252:99:7584,545,0:60:99:1.000
chr3	167097421	rs13073265	C	T	8409.69	PASS	DP=296;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=11.7942;MQ=60;MQ0=0;QD=28.41;SB=-4230.24;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Silent,Silent,Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,296:296:99:8410,602,0:60:99:1.000
chr3	169557842	rs16854445	C	T	8321.67	PASS	DP=276;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=8.0976;MQ=60;MQ0=0;QD=30.15;SB=-4841.56;TI=NM_024727;GI=LRRC31;FC=Synonymous_Q529Q;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,275:276:99:8322,605,0:60:99:1.000
chr3	169558025	rs3732451	C	T	16520.50	PASS	DP=598;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=21.2875;MQ=60;MQ0=0;QD=27.63;SB=-10959.81;TI=NM_024727;GI=LRRC31;FC=Synonymous_A468A;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,596:598:99:16520,1177,0:60:99:1.000
chr3	169566090	rs9290375	A	G	6650.69	PASS	DP=223;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=9.0410;MQ=60;MQ0=0;QD=29.82;SB=-2599.99;TI=NM_024727;GI=LRRC31;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,223:223:99:6651,482,0:60:99:1.000
chr3	169569432	rs35923425	C	G	8580.88	PASS	DP=299;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=9.0306;MQ=60;MQ0=0;QD=28.70;SB=-4150.05;TI=NM_024727;GI=LRRC31;FC=Missense_L378F;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,298:299:99:8581,614,0:60:99:1.000
chr3	180332171	.	T	G	68.24	SB	BaseQRankSum=-3.736;DP=164;Dels=0.01;FS=104.875;HRun=7;HaplotypeScore=82.2022;MQ=59;MQ0=0;MQRankSum=-0.843;QD=0.42;ReadPosRankSum=-0.322;SB=-0.01;TI=NM_181426;GI=CCDC39;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:121,39:163:98.23:98,0,2250:59:68:0.244
chr3	180379648	.	C	G	3891.77	PASS	DP=130;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=6.3619;MQ=60;MQ0=0;QD=29.94;SB=-1485.61;TI=NM_181426;GI=CCDC39;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,130:130:99:3892,280,0:60:99:1.000
chr3	180565309	rs6443724	T	A	7732.14	PASS	BaseQRankSum=1.683;DP=281;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=16.1001;MQ=60;MQ0=0;MQRankSum=-0.918;QD=27.52;ReadPosRankSum=1.633;SB=-4626.45	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:1,280:281:99:7732,551,0:60:99:0.996
chr3	180565417	.	GA	G	603.70	LowVariantFreq;R8	BaseQRankSum=1.440;DP=320;FS=0.456;HRun=14;HaplotypeScore=841.5623;MQ=60;MQ0=0;MQRankSum=-0.690;QD=1.89;ReadPosRankSum=-0.011;SB=-258.65	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:233,58:320:99:643,0,4489:60:99:0.199
chr3	197659160	rs67877771	C	G	1161.32	PASS	BaseQRankSum=0.614;DP=176;Dels=0.00;FS=2.032;HRun=1;HaplotypeScore=5.3371;MQ=60;MQ0=0;MQRankSum=1.573;QD=6.60;ReadPosRankSum=-2.257;SB=-672.70;TI=NM_032263,NM_001134435;GI=IQCG,IQCG;FC=Missense_D177H,Missense_D177H;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:122,54:176:99:1191,0,2922:60:99:0.307
chr3	197665599	rs9880989	G	T	4950.19	PASS	BaseQRankSum=1.339;DP=413;Dels=0.00;FS=0.356;HRun=0;HaplotypeScore=13.9140;MQ=60;MQ0=0;MQRankSum=0.431;QD=11.99;ReadPosRankSum=-0.106;SB=-3430.57;TI=NM_032263,NM_001134435;GI=IQCG,IQCG;FC=Missense_A112D,Missense_A112D;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:199,213:413:99:4950,0,4906:60:99:0.517
chr4	185999543	rs6841061	G	A	1745.43	PASS	BaseQRankSum=1.028;DP=267;Dels=0.00;FS=3.769;HRun=3;HaplotypeScore=9.1209;MQ=60;MQ0=0;MQRankSum=-0.581;QD=6.54;ReadPosRankSum=2.564;SB=-1166.85	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:186,80:267:99:1775,0,4576:60:99:0.301
chr5	10442068	rs1047426	C	T	9768.98	PASS	DP=359;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=17.1759;MQ=60;MQ0=0;QD=27.21;SB=-4873.83;TI=NM_031916;GI=ROPN1L;FC=Silent;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	1/1:0,357:357:99:9769,695,0:60:99:1.000
chr5	10442427	rs78035767	C	G	6644.46	PASS	BaseQRankSum=2.821;DP=622;Dels=0.00;FS=6.185;HRun=4;HaplotypeScore=30.6702;MQ=60;MQ0=0;MQRankSum=-0.724;QD=10.68;ReadPosRankSum=0.182;SB=-3228.09;TI=NM_031916;GI=ROPN1L;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:343,278:622:99:6644,0,8052:60:99:0.448
chr5	10448505	rs11957839	G	C	4899.84	PASS	BaseQRankSum=2.259;DP=357;Dels=0.00;FS=2.362;HRun=0;HaplotypeScore=13.7716;MQ=60;MQ0=0;MQRankSum=0.073;QD=13.73;ReadPosRankSum=0.796;SB=-2462.92;TI=NM_031916;GI=ROPN1L;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:159,198:357:99:4900,0,3715:60:99:0.555
chr5	13769257	rs12655133	T	A	4121.37	PASS	BaseQRankSum=0.389;DP=335;Dels=0.00;FS=16.036;HRun=3;HaplotypeScore=12.6576;MQ=60;MQ0=0;MQRankSum=-0.254;QD=12.30;ReadPosRankSum=2.203;SB=-2868.34;TI=NM_001369;GI=DNAH5;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:154,179:334:99:4121,0,3942:60:99:0.538
chr5	13788886	rs10513155	C	A	4436.38	PASS	BaseQRankSum=1.585;DP=476;Dels=0.00;FS=0.698;HRun=2;HaplotypeScore=16.2312;MQ=60;MQ0=0;MQRankSum=-0.937;QD=9.32;ReadPosRankSum=-1.920;SB=-3181.08;TI=NM_001369;GI=DNAH5;FC=Missense_L2862F;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:278,198:476:99:4436,0,6660:60:99:0.416
chr5	13842027	.	C	CA	281.78	R8	BaseQRankSum=-1.335;DP=100;FS=0.000;HRun=19;HaplotypeScore=483.5337;MQ=60;MQ0=0;MQRankSum=2.284;QD=2.82;ReadPosRankSum=-1.057;SB=-112.79;TI=NM_001369;GI=DNAH5;FC=Noncoding	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:50,23:100:99:319,0,302:60:99:0.315
chr5	13850750	rs6554820	A	G	4631.11	PASS	BaseQRankSum=-0.018;DP=394;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=12.5955;MQ=60;MQ0=0;MQRankSum=-0.114;QD=11.75;ReadPosRankSum=-0.614;SB=-2914.77;TI=NM_001369;GI=DNAH5;FC=Silent	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:195,199:394:99:4631,0,4452:60:99:0.505
chr5	13864728	rs6554827	C	A	3760.61	PASS	BaseQRankSum=2.300;DP=365;Dels=0.00;FS=15.132;HRun=0;HaplotypeScore=24.6423;MQ=60;MQ0=0;MQRankSum=-0.095;QD=10.30;ReadPosRankSum=-2.326;SB=-1734.26;TI=NM_001369;GI=DNAH5;FC=Synonymous_R1458R;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:211,152:365:99:3761,0,4954:60:99:0.419
chr5	13865980	rs7703349	T	C	3680.40	PASS	BaseQRankSum=2.457;DP=313;Dels=0.00;FS=1.881;HRun=0;HaplotypeScore=9.5836;MQ=60;MQ0=0;MQRankSum=1.151;QD=11.76;ReadPosRankSum=-0.725;SB=-2385.32;TI=NM_001369;GI=DNAH5;FC=Synonymous_T1384T;EXON	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:154,159:313:99:3680,0,3513:60:99:0.508
chr5	13868103	.	TA	T	3785.47	R8	BaseQRankSum=1.577;DP=333;FS=1.354;HRun=9;HaplotypeScore=256.0566;MQ=60;MQ0=0;MQRankSum=-1.387;QD=11.37;ReadPosRankSum=2.046;SB=-1481.62;TI=NM_001369;GI=DNAH5;FC=Splicing	GT:AD:DP:GQ:PL:MQ:GQX:VF	0/1:177,147:333:99:3785,0,4159:60:99:0.454
chr5	13882841	rs10057007	A	G	1269.82	PASS	BaseQRankSum=1.571;DP=232;Dels=0.00;FS=15.789;HRun=1;HaplotypeScore=5.5137;MQ=60;MQ0=0;MQRankSum=-0.392;QD=5.47;ReadPo